PyMOL is a great program that runs natively on all 3 major platforms. However, I wanted to use a docker image that allegedly can run PyMOL (albeit an older version 1.8.2.) The reason might not be apparent at first but while the 3D interactivity would be slow, there can be other reason such a contraption …
This is a list of R material that I found online that I think can be useful as reference or as working material to learn R / RStudio / Mardkown. I’ll try to separate the links between “Classic” and “Tidyverse” versions, but that is not always possible… “Tidyverse” would include plotting with ggplot2 R package which …
Tabular formats When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to work with sequences was the (now defunct GCG) program REFORMAT. And “boy” was he right, as in my 30+ years …
In 1992 I attended a molecular graphics visualization and simulation somewhere in Texas, organized by Keck. One of the presenter had a movie of molecular dynamics of a protein that forever changed my mental view of the 3D structure of a protein: the atoms “wiggled” and it made clear with a stunning visual depiction that …
PyMOL license needs update Attention PyMOL users. The UW license is set to expire on January 15th, 2020. The license is required for running PyMOL starting with version 2.o and works for now on all updated 2.x versions (currently 2.3.4.) Edit: for Departmental computer Biochem IT is “pushing” the license to departmental computers, hence this …
Winter 2020 Programming Workshops on Campus In the past years I have offered python 3, R, and RStudio workshops within the Biochem Department (see links below.) R is both a language and a software environment for statistical computing and graphics. R (and other languages) can be used through the amazing RStudio interface for even more performance, ease …
Reproducible research Docker is a great tool to provide methods for reproducible research that should allow other researchers to reproduce any advanced calculations that you, as a researcher have done, most likely in association with publishing a paper. However, there are many caveats along the way, the first one being explanations on how to launch …
A couple years ago I wrote a short note on another blog (DNA.today – link below) about a web site that can be quite useful: it provides the name of alternate software. The site is: alternativeto.net For example, if you cannot afford Adobe PhotoShop you would be glad to find an alternative in “Gimp” (GNU Image Manipulation Program.) The …
The built-in Terminal in MacOS and Linux and in Windows with added software provides access to the core of the computer. They are simply a software version (an emulation) of what used to be a hardware terminal (as the one shown above) user to connect to a computer when these were the size of multiple washing …
Edit: April 8, 2025 Images were updated to remove the error that presented the roadmap in a mirror image. Docker saves the day! Here is a great example of how Docker can help save a NATURE paper! Summary: Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works on …